It's alright, tension is pretty subtle! Let me answer your questions a bit out of order.
- If you pick any and all points on the rope, would there be two opposing tensions at every one of those points?
- Is tension uniform throughout the rope?
You can think about the rope as a lot of tiny masses connected together by springs; this is a cheap approximation for how tension works on the atomic level, where the springs are stretching chemical bonds and the masses are atoms.
In our simple model of tension, every atom is pulled by a spring on the left and a spring on the right, with forces $T_1$ and $T_2$. Then by Newton's second law,
$$T_1 - T_2 = ma$$
where $m$ is the mass of the atom. Since $m$ is very very tiny compared to the other masses in the problem, we must have
$$T_1 \approx T_2.$$
Applying this to every mass, we conclude that each little spring / chemical bond has approximately the same tension, so we can simply talk about "the tension in the rope". This is a good approximation as long as the total mass of the rope is much smaller than the masses of the blocks.
How might differences in mass between object A and object B (which, sorry if the diagram was misleading in the sizes, can have any mass) play into the tension?
Well, now that we've established that there's a uniform tension $T$, we need to figure out what that tension is. The constraint here is that the rope is taut, which means that it can't be scrunching up or stretching out; that translates to the constraint that the accelerations of the two blocks are equal in magnitude. This equation determines the tension.
How does the relationship between the force of gravity on mass B and the tension in the rope play into this? Isn't the tension caused by that force of gravity? Doesn't that mean that if tensions cancel, the force of gravity's effect is canceled as well?
(I have also been told that the blocks will have the same magnitude of acceleration. Why is this?)
No, the tension isn't equal to the weight of block B, it's whatever is necessary to satisfy the above constraint. For example, suppose that block B was very very heavy, so the acceleration of the whole system will be close to $g$. In this case, the tension is actually quite small compared to the weight of block B, because you only need a little tension to make block A have the same acceleration.
(In fact, as block B gets infinitely heavy, you can show that the tension doesn't go to infinity -- instead, it becomes the weight of block A! It's neat to try to prove this, and see how it works.)
Does the pulley affect tensions? For example, we know that there's a positive tension affecting mass A. Is there still a positive tension in existence on the other side of the pulley, or just the negative tension that's acting on B? Might there be some sort of effect whereby two sets of opposite tensions, one set on each side of the pulley, cancel each other out?
This is a little tricky to word. The tensions of the two tiny springs attached to each atom approximately cancel out, as shown above. But that doesn't mean that the tension is zero -- all of those springs are still stretched.
Since the pulley is frictionless, it doesn't have any effect except that it 'turns around' the tension. You can show this by considering the three forces on each atom (two springs, one normal force) which gives $T_1 \approx T_2$ as before.
Anyway, I've been told that the net force is the force of gravity on mass B (the hanging one). But I don't really understand why, even after extensive discussion with various people.
That's not your fault, the question is just worded badly. There are lots of forces involved in this problem acting on different things: gravity on both blocks, normal on one block, and normal from the pulley on the rope. It's not very clear what "the" net force even means.
Best Answer
It is all a matter of progression.
When one starts studying Mechanics it is in terms of point masses, massless and inextensible strings, frictionless and massless pulleys, etc..
This is done to produce some foundations on which to build.
Strings and pulleys are just devices for transferring forces from one place to another and changing the directions of forces.
A step forward is to introduce rotational dynamics where bodies are no longer treated as point masses and pulleys suddenly become nearer to those that can be found in the real world.
It appears that you have taken such a step.
If you have a pulley of moment of inertia $I_{\rm C}$ about its centre of mass then to produce an angular acceleration $\alpha$ of the pulley requires a torque about the centre of mass of the pulley of $\tau = I_{\rm C} \;\alpha$.
Note that if the pulley is massless then it has no moment of inertia and so requires no torque to accelerate it.
The torque is applied using a string which can still be assumed massless and inextensible but now communicates with the pulley via a static frictional force.
This now means that the tension in the string is no longer constant as is shown in the solution to the capstan problem. (However note that there are no accelerations in the derivation).
You normally do not worry about the detail of the interaction between the pulley and the string what interests you is the fact that the tensions at either end of the string are difference and it is that difference which enable the string to apply a torque on the pulley.
In some cases you could assume that the moment of inertia of the pulley is so small as to make the very little difference to the tension in the string which is mirroring the assumption that the pulley is massless.
I wonder what assumptions (simplifications) NASA made when designing their pulley system?